refactor: use attributes

[xgui3783]

supercedes https://github.com/FZJ-INM1-BDA/siibra-python/pull/553

EDIT: The tests are turned off, except for the ones in examples_new to see if there is regression. The remaining test migration will be made gradually. (b70abe9f03533c684207462d5407dee96bed459d and 8a47f0feff6d6bd760ddce3e1ba0df1246c0955a)

[xgui3783]

attn @AhmetNSimsek

per our discussion, here is the WIP

left to do:

refactor todo list

• [x] implement {method}_iter()
• [ ] atlas elements
  • [x] space
  • [x] parcellation
    • [x] class
    • [x] get_region()
  • [ ] region
    • [x] class
    • [x] find()
    • [x] top_most flag
    • [x] get_regional_map()
  • [x] parcellation map @AhmetNSimsek
  • [x] labelled
  • [x] statistical
• [x] update siibra/attr/meta/doi -> siibra/attr/desc/url see https://github.com/FZJ-INM1-BDA/siibra-configurations/commit/9806628c4a6e9dec04627622c61665dee15314c9
  • [x] update schema
  • [x] update key url -> value
• [x] update siibra/attr/data/voi -> siibra/attr/data/image see https://github.com/FZJ-INM1-BDA/siibra-configurations/commit/9806628c4a6e9dec04627622c61665dee15314c9
  • [x] update schema
• [x] update regionspec see https://github.com/FZJ-INM1-BDA/siibra-configurations/commit/9806628c4a6e9dec04627622c61665dee15314c9
  • [x] fix property key name -> value
• [ ] port over features
  • [x] connectivity
  • [ ] bold @AhmetNSimsek
  • [x] live queries
  • [x] allen see https://github.com/FZJ-INM1-BDA/siibra-python/blob/e2c5284f6a1f85a70556b583944339e26d960386/siibra/retrieval_new/api_fetcher/allen.py and https://github.com/FZJ-INM1-BDA/siibra-python/blob/e2c5284f6a1f85a70556b583944339e26d960386/foo.py#L68-L82
  • [x] big brain intensity profile see https://github.com/FZJ-INM1-BDA/siibra-python/pull/594/commits/d22f454cab6ac03e535913f2be1c4afe10da84cf
  • [x] brainglobe
  • [x] document how to add additional external connectors see https://github.com/FZJ-INM1-BDA/siibra-python/pull/594/commits/d22f454cab6ac03e535913f2be1c4afe10da84cf
  • [x] reimplement autocomplete all modalities see https://github.com/FZJ-INM1-BDA/siibra-python/pull/594/commits/44a7194ef04da61b652367010b884f3a91a70978
  • [x] sample feature fetching see https://github.com/FZJ-INM1-BDA/siibra-python/pull/594/commits/44a7194ef04da61b652367010b884f3a91a70978
• [x] move cache to root level module
• [x] attr
  • [x] image dataitem (Image subclassing Location) @AhmetNSimsek
  • [x] add more attr comparison
  • [x] regionspec match @AhmetNSimsek
  • [x] Bbox to bbox see https://github.com/FZJ-INM1-BDA/siibra-python/pull/594/commits/6bb174ebc9678d035e72e9523a55795b5e3ee4d5
  • [x] ptcloud (and pt) to image
• [x] setup & test siibra-schema repo see https://github.com/FZJ-INM1-BDA/siibra-schema
• [ ] consider using standard json-ld schema, context etc
• [ ] Retrieval
  • [ ] Volume Fetcher @AhmetNSimsek
  • [x] NiftiFetcher
  • [x] NeuroglancerFetcher
  • [ ] NeuroglancerMeshFetcher
  • [x] GiftiFetcher
  • [x] FreesurferAnnotFetcher
  • [ ] File fetcher
    • [x] LocalFile Fetcher @xgui3783
    • [x] zip fetcher
    • [x] tar fetcher
    • [x] Github fetcher @xgui3783
    • [x] Gitlab fetcher @xgui3783
    • [ ] EBRAINS fetcher ?
    • [ ] owncloud?
  • [ ] Locations @AhmetNSimsek
    • [ ] boundingbox
    • [ ] pointcloud
      • [ ] contour
    • [ ] point
    • [ ] plane3d
    • [ ] polyline
• [ ] Map assignment
  • [ ] Point and PointCloud (etc) assignment to labelled and statistical maps
  • [ ] Image assignment to maps
• [ ] Unit tests
• [ ] e2e tests (For now, we are using foos under examples to test along with migrated/translated examples)
• [ ] Examples
• [ ] Notebooks to reproduce code on siibra paper
• [ ] Polish docs (Need to discuss)

[AhmetNSimsek]

region.find is not deterministic and rather slow. I am noting down to investigate later.

[AhmetNSimsek]

@xgui3783, I think we should remove the dataclass decorators from classes that inherit other a class that has a dataclass decorator. Because it creates unexpected behaviors such as some methods are overridden and very difficult to debug as it is an unexpected behavior. Regarding being explicit: if a class A inherits a class B with dataclass decorators, the developer would know that A is also a dataclass. So, by repeating the 2 lines required to decorate class A as a dataclass, we break DRY, we face unexpected behavior, and we don't gain anything besides being explicit which is not really necessary in this context.

This changes if the class has extra members. Then, it is needed to use the decorator as the __init__ needs to be overridden. I suggest we remove all we can and leave only the necessary implementations. What do you think?